Turns out the source of many germs in a hotel room is the air conditioning unit. 

The filters need to be cleaned at least 4 times a year and, if they are not, you could be breathing in noxious air. 

According to this article, a rise in flu has been linked to dirty air conditioning units. 

It does make you think about all places AC is in common use - most offices for example now have AC. Could explain a lot of absenteeism.